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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctcttcaattttttgttgtcatgcgtctctgttctctggatggccttaacacattgttgtccacttctcatag

Basic information

species Oryza sativa
transcript LOC_Os02g57630.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G108739_T01 (Zea mays), 5'ss of exon 4
GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctcttcaattttt-tgttgtcatgcgtctctgttctctggatggccttaacacattgttgtcc-----acttctcatag
|||||||| ||||||||||| ||||||| |||| ||||| ||||||||||||  |||| | | ||| ||| |||||   | ||||   |||| ||| | | |||||||  ||||||     |||| || |||
GTGGAAGAGCTTTACTCTCTCGATGTGGGCTCTCTTAGTCAACTGCGgtgagaatctttattatttatgtcgtcat---tatctgcaatctgaatgccttgaacacatatttgtcctctccacttttcttag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|699770|gb|D46061.1|D46061
EST:     GAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTNCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|29668373|gb|CB664648.1|CB664648
EST:     GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|25798730|gb|CA754699.1|CA754699
EST:     GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|699786|gb|D46077.1|D46077
EST:     GAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTNCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|218484923|gb|FG943842.1|FG943842
EST:     GTGGAAGAACTTTACTCTCTTAGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GTGGAAGAACTTTACTCTCTT-GATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|29668412|gb|CB664687.1|CB664687
EST:     GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|218495715|gb|FG959020.1|FG959020
EST:     AGTGAACTGCG                         G-CAG-TTATGGGCT-ATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: AGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
EST: gi|33797877|gb|CF324798.1|CF324798
EST:     GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCG                         GCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA
genomic: GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctct ... cttctcatagGCCAGTTTATGGGCTAATTTTTCTCTTCAAGTGGATGGCTGGGGAAAAGGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAAGAACTTTACTCTCTTGATGTGGACTCTATTAGTGAACTGCGgtgagtctcttcaattttttgttgtcatgcgtctctgttctctggatggccttaacacattgttgtccacttctcatag

 TGGAAG
- GGAAGA
- - AAGAAC